Ace.py

# Copyright 2004 by Frank Kauff and Cymon J. Cox. All rights reserved.# This code is part of the Biopython distribution and governed by its# license. Please see the LICENSE file that should have been included# as part of this package."""Parser for ACE files output by PHRAP.Written by Frank Kauff (fkauff@duke.edu) andCymon J. Cox (cymon@duke.edu)Uses the Biopython Parser interface: ParserSupport.pyUsage:There are two ways of reading an ace file:1) The function 'read' reads the whole file at once;2) The function 'parse' reads the file contig after contig.1) Parse whole ace file at once: from Bio.Sequencing import Ace acefilerecord=Ace.read(open('my_ace_file.ace'))This gives you: acefilerecord.ncontigs (the number of contigs in the ace file) acefilerecord.nreads (the number of reads in the ace file) acefilerecord.contigs[] (one instance of the Contig class for each contig)The Contig class holds the info of the CO tag, CT and WA tags, and all the reads usedfor this contig in a list of instances of the Read class, e.g.: contig3=acefilerecord.contigs[2] read4=contig3.reads[3] RD_of_read4=read4.rd DS_of_read4=read4.dsCT, WA, RT tags from the end of the file can appear anywhere are automaticallysorted into the right place.see _RecordConsumer for details.2) Or you can iterate over the contigs of an ace file one by one in the ususal way: from Bio.Sequencing import Ace contigs=Ace.parse(open('my_ace_file.ace')) for contig in contigs: print contig.name ...Please note that for memory efficiency, when using the iterator approach, only onecontig is kept in memory at once. However, there can be a footer to the ACE filecontaining WA, CT, RT or WR tags which contain additional meta-data on the contigs.Because the parser doesn't see this data until the final record, it cannot be added tothe appropriate records. Instead these tags will be returned with the last contig record.Thus an ace file does not entirerly suit the concept of iterating. If WA, CT, RT, WR tagsare needed, the 'read' function rather than the 'parse' function might be more appropriate."""00060class rd:
"""RD (reads), store a read with its name, sequence etc."""def __init__(self):
self.name=''
self.padded_bases=None
self.info_items=None
self.read_tags=None
self.sequence=''00069class qa:
"""QA (read quality), including which part if any was used as the consensus."""def __init__(self, line=None):
self.qual_clipping_start=None
self.qual_clipping_end=None
self.align_clipping_start=None
self.align_clipping_end=Noneif line:
header=map(eval,line.split()[1:])
self.qual_clipping_start=header[0]
self.qual_clipping_end=header[1]
self.align_clipping_start=header[2]
self.align_clipping_end=header[3]
00083class ds:
"""DS lines, include file name of a read's chromatogram file."""def __init__(self, line=None):
self.chromat_file=''
self.phd_file=''
self.time=''
self.chem=''
self.dye=''
self.template=''
self.direction=''if line:
tags=['CHROMAT_FILE','PHD_FILE','TIME','CHEM','DYE','TEMPLATE','DIRECTION']
poss=map(line.find,tags)
tagpos=dict(zip(poss,tags))
if -1 in tagpos:
del tagpos[-1]
ps=tagpos.keys()
ps.sort()
for (p1,p2) in zip(ps,ps[1:]+[len(line)+1]):
setattr(self,tagpos[p1].lower(),line[p1+len(tagpos[p1])+1:p2].strip())
00105class af:
"""AF lines, define the location of the read within the contig."""def __init__(self, line=None):
self.name=''
self.coru=None
self.padded_start=Noneif line:
header = line.split()
self.name = header[1]
self.coru = header[2]
self.padded_start = int(header[3])
00117class bs:
""""BS (base segment), which read was chosen as the consensus at each position."""def __init__(self, line=None):
self.name=''
self.padded_start=None
self.padded_end=Noneif line:
header = line.split()
self.padded_start = int(header[1])
self.padded_end = int(header[2])
self.name = header[3]
00129class rt:
"""RT (transient read tags), generated by crossmatch and phrap."""def __init__(self, line=None):
self.name=''
self.tag_type=''
self.program=''
self.padded_start=None
self.padded_end=None
self.date=''if line:
header=line.split()
self.name=header[0]
self.tag_type=header[1]
self.program=header[2]
self.padded_start=int(header[3])
self.padded_end=int(header[4])
self.date=header[5]
00147class ct:
"""CT (consensus tags)."""def __init__(self, line=None):
self.name=''
self.tag_type=''
self.program=''
self.padded_start=None
self.padded_end=None
self.date=''
self.notrans=''
self.info=[]
self.comment=[]
if line:
header=line.split()
self.name = header[0]
self.tag_type = header[1]
self.program = header[2]
self.padded_start = int(header[3])
self.padded_end = int(header[4])
self.date = header[5]
if len(header)==7:
self.notrans = header[6]
00170class wa:
"""WA (whole assembly tag), holds the assembly program name, version, etc."""def __init__(self, line=None):
self.tag_type=''
self.program=''
self.date=''
self.info=[]
if line:
header = line.split()
self.tag_type = header[0]
self.program = header[1]
self.date = header[2]
00183class wr:
"""WR lines."""def __init__(self, line=None):
self.name=''
self.aligned=''
self.program=''
self.date=[]
if line:
header = line.split()
self.name = header[0]
self.aligned = header[1]
self.program = header[2]
self.date = header[3]
00197class Reads:
"""Holds information about a read supporting an ACE contig."""def __init__(self, line=None):
self.rd=None# one per read
self.qa=None# one per read
self.ds=None# none or one per read
self.rt=None# none or many per read
self.wr=None# none or many per readif line:
self.rd = rd()
header = line.split()
self.rd.name = header[1]
self.rd.padded_bases = int(header[2])
self.rd.info_items = int(header[3])
self.rd.read_tags = int(header[4])
00213class Contig:
"""Holds information about a contig from an ACE record."""def __init__(self, line=None):
self.name = ''
self.nbases=None
self.nreads=None
self.nsegments=None
self.uorc=None
self.sequence=""
self.quality=[]
self.af=[]
self.bs=[]
self.reads=[]
self.ct=None# none or many
self.wa=None# none or manyif line:
header = line.split()
self.name = header[1]
self.nbases = int(header[2])
self.nreads = int(header[3])
self.nsegments = int(header[4])
self.uorc = header[5]
def parse(handle):
"""parse(handle) where handle is a file-like object. This function returns an iterator that allows you to iterate over the ACE file record by record: records = parse(handle) for record in records: # do something with the record where each record is a Contig object. """
handle = iter(handle)
line = ""whileTrue:
# at beginning, skip the AS and look for first CO commandtry:
whileTrue:
if line.startswith('CO'):
break
line = handle.next()
except StopIteration:
return
record = Contig(line)
for line in handle:
line = line.strip()
ifnot line:
break
record.sequence+=line
for line in handle:
if line.strip():
breakifnot line.startswith("BQ"):
raise ValueError("Failed to find BQ line")
for line in handle:
ifnot line.strip():
break
record.quality.extend(map(int,line.split()))
for line in handle:
if line.strip():
breakwhileTrue:
ifnot line.startswith("AF "):
break
record.af.append(af(line))
try:
line = handle.next()
except StopIteration:
raise ValueError("Unexpected end of AF block")
whileTrue:
if line.strip():
breaktry:
line = handle.next()
except StopIteration:
raise ValueError("Unexpected end of file")
whileTrue:
ifnot line.startswith("BS "):
break
record.bs.append(bs(line))
try:
line = handle.next()
except StopIteration:
raise ValueError("Failed to find end of BS block")
# now read all the read data# it starts with a 'RD', and then a mandatory QA# then follows an optional DS# CT,RT,WA,WR may or may not be there in unlimited quantity. They might refer to the actual read or contig,# or, if encountered at the end of file, to any previous read or contig. the sort() method deals# with that later.whileTrue:
# each read must have a rd and qatry:
whileTrue:
# If I've met the condition, then stop reading the line.if line.startswith("RD "):
break
line = handle.next()
except StopIteration:
raise ValueError("Failed to find RD line")
record.reads.append(Reads(line))
for line in handle:
line = line.strip()
ifnot line:
break
record.reads[-1].rd.sequence+=line
for line in handle:
if line.strip():
breakifnot line.startswith("QA "):
raise ValueError("Failed to find QA line")
record.reads[-1].qa = qa(line)
# now one ds can followfor line in handle:
if line.strip():
breakelse:
breakif line.startswith("DS "):
record.reads[-1].ds = ds(line)
line = ""# the file could just end, or there's some more stuff. In ace files, anything can happen.# the following tags are interspersed between reads and can appear multiple times. whileTrue:
# something left try:
whileTrue:
if line.strip():
break
line = handle.next()
except StopIteration:
# file ends herebreakif line.startswith("RT{"):
# now if we're at the end of the file, this rt could# belong to a previous read, not the actual one.# we store it here were it appears, the user can sort later.if record.reads[-1].rt isNone:
record.reads[-1].rt=[]
for line in handle:
line=line.strip()
if line=='}': break
record.reads[-1].rt.append(rt(line))
line = ""elif line.startswith("WR{"):
if record.reads[-1].wr isNone:
record.reads[-1].wr=[]
for line in handle:
line=line.strip()
if line=='}': break
record.reads[-1].wr.append(wr(line))
line = ""elif line.startswith("WA{"):
if record.wa isNone:
record.wa=[]
try:
line = handle.next()
except StopIteration:
raise ValueError("Failed to read WA block")
record.wa.append(wa(line))
for line in handle:
line=line.strip()
if line=='}': break
record.wa[-1].info.append(line)
line = ""elif line.startswith("CT{"):
if record.ct isNone:
record.ct=[]
try:
line = handle.next()
except StopIteration:
raise ValueError("Failed to read CT block")
record.ct.append(ct(line))
for line in handle:
line=line.strip()
if line=="COMMENT{":
for line in handle:
line = line.strip()
if line.endswith("C}"):
break
record.ct[-1].comment.append(line)
elif line=='}':
breakelse:
record.ct[-1].info.append(line)
line = ""else:
breakifnot line.startswith('RD'): # another read?breakyield record
00429class ACEFileRecord:
"""Holds data of an ACE file. """def __init__(self):
self.ncontigs=None
self.nreads=None
self.contigs=[]
self.wa=None# none or many00438def sort(self):
"""Sorts wr, rt and ct tags into the appropriate contig / read instance, if possible. """
ct=[]
rt=[]
wr=[]
# search for tags that aren't in the right positionfor i in range(len(self.contigs)):
c = self.contigs[i]
if c.wa:
ifnot self.wa:
self.wa=[]
self.wa.extend(c.wa)
if c.ct:
newcts=[ct_tag for ct_tag in c.ct if ct_tag.name!=c.name]
map(self.contigs[i].ct.remove,newcts)
ct.extend(newcts)
for j in range(len(c.reads)):
r = c.reads[j]
if r.rt:
newrts=[rt_tag for rt_tag in r.rt if rt_tag.name!=r.rd.name]
map(self.contigs[i].reads[j].rt.remove,newrts)
rt.extend(newrts)
if r.wr:
newwrs=[wr_tag for wr_tag in r.wr if wr_tag.name!=r.rd.name]
map(self.contigs[i].reads[j].wr.remove,newwrs)
wr.extend(newwrs)
# now sort them into their proper placefor i in range(len(self.contigs)):
c = self.contigs[i]
for ct_tag in ct:
if ct_tag.name==c.name:
if self.contigs[i].ct isNone:
self.contigs[i].ct=[]
self.contigs[i].ct.append(ct_tag)
if rt or wr:
for j in range(len(c.reads)):
r = c.reads[j]
for rt_tag in rt:
if rt_tag.name==r.rd.name:
if self.contigs[i].reads[j].rt isNone:
self.contigs[i].reads[j].rt=[]
self.contigs[i].reads[j].rt.append(rt_tag)
for wr_tag in wr:
if wr_tag.name==r.rd.name:
if self.contigs[i].reads[j].wr isNone:
self.contigs[i].reads[j].wr=[]
self.contigs[i].reads[j].wr.append(wr_tag)
def read(handle):
"""Parses the full ACE file in list of contigs. """
handle = iter(handle)
record=ACEFileRecord()
try:
line = handle.next()
except StopIteration:
raise ValueError("Premature end of file")
# check if the file starts correctlyifnot line.startswith('AS'):
raise ValueError("File does not start with 'AS'.")
words = line.split()
record.ncontigs, record.nreads = map(int, words[1:3])
# now read all the records
record.contigs = list(parse(handle))
# wa, ct, rt rags are usually at the end of the file, but not necessarily (correct?).# If the iterator is used, the tags are returned with the contig or the read after which they appear,# if all tags are at the end, they are read with the last contig. The concept of an# iterator leaves no other choice. But if the user uses the ACEParser, we can check# them and put them into the appropriate contig/read instance.# Conclusion: An ACE file is not a filetype for which iteration is 100% suitable...
record.sort()
return record